Epitope vaccines based on the dynamics of mutated SARS-CoV-2 proteins at all-atom resolution

Epitope vaccines based on the dynamics of mutated SARS-CoV-2 proteins at all-atom resolution is a PRACE-awarded project led by Prof. Evangelos Daskalakis from the Cyprus University of Technology, Cyprus. The working hypothesis of Daskalakis' team is that the research on SARS-CoV-2 should focus on proteins that exhibit higher evolutionary conservation and lower mutation rates as these could be potential drug targets or sources of epitopes. These epitopes, which derive from the spike of the virus, and nucleocapsid proteins, could potentially offer protection against the coronavirus by mapping identically to SARS-CoV-2 proteins. The reason is that epitopes are part of an antigen that is recognized by the immune system, specifically by antibodies, B-cells, or T-cells. The project's computational approach advances scientific knowledge on SARS-CoV-2 at the fundamental level. The results will take the form of important protein domains in wild-type, i.e. unchanged, or mutants that could be directly associated with epitopes for eventual vaccines against COVID-19. Of course, they could be further used in protein-drug docking algorithms to predict drug efficiency, and support the engineering of vaccines. The project focusses on characterising the molecular features associated with the virus (proteins, genetic material) at all-atom resolution. For this the scientists will conduct a screening of a large database of natural products to find potential inhibitors that bind at the key protein domains. They also plan to propose novel molecules as potential inhibitors to block the virus. All these fundamental studies require enormous computational power and PRACE awarded the project of Prof. Evangelos Daskalakis with 16 000 000 core hours on Joliot-Curie Rome, hosted by GENCI at CEA, France.